Question: Ambigious sex warning using PLINK
gravatar for kris_A
4.1 years ago by
New Zealand
kris_A40 wrote:

Hello everyone,

I am using PLINK to process SNP data. I'm new to using this toolset and performing such analyses and was hoping someone could help me out with this. After running the initial function of converting the .map and .ped files into binary, I get a warning in the log that all individuals I am processing have an ambiguous sex code.

After filtering, 0 cases, 0 controls and 134 missing After filtering, 0 males, 0 females, and 134 of unspecified sex

I cannot find anywhere if that is in issue for further analyses and what I can do to fix it. Thank you for your help.

Best, Kristina

nosex snp plink analysis • 2.5k views
ADD COMMENTlink written 4.1 years ago by kris_A40

From the message, it appears PLINK is not recognizing the sex coding in your dataset. As first check, in your input .ped file, are you coding sex in the 5th column using the PLINK standard 1=male, 2=female, 0=unknown? See here. If sex is unknown in your input dataset, you can still continue with analyses that don't depend on having that information.

ADD REPLYlink written 4.1 years ago by Ahill1.9k

Ok! yes, completely makes sense, as it is actually unknown in that data set. Thank you for pointing out the obvious I was failing to recognize !

ADD REPLYlink written 4.1 years ago by kris_A40
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